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- PDB-9xfw: Crystal structure of Class A beta-lactamase BlaA in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9xfw
TitleCrystal structure of Class A beta-lactamase BlaA in complex with Meropenem (Imine form)
ComponentsBeta-lactamase
KeywordsHYDROLASE / Partial Carbapenemase / Acy-Enzyme Complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-DWZ / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBhattachaya, S. / Dhankhar, K. / Hazra, S.
Funding support India, 2items
OrganizationGrant numberCountry
Indian Council of Medical Research India
Board of Research in Nuclear Sciences (BRNS) India
CitationJournal: To Be Published
Title: Crystal structure of Class A beta-lactamase BlaA in complex with Meropenem (Imine form)
Authors: Bhattachaya, S. / Dhankhar, K. / Hazra, S.
History
DepositionOct 29, 2025Deposition site: PDBJ / Processing site: PDBJ
SupersessionNov 12, 2025ID: 8IY4
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4473
Polymers31,9671
Non-polymers4802
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-3 kcal/mol
Surface area11180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.774, 72.619, 43.707
Angle α, β, γ (deg.)90, 94.953, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

21A-523-

HOH

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Components

#1: Protein Beta-lactamase / Penicillinase


Mass: 31966.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: blaA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01166, beta-lactamase
#2: Chemical ChemComp-DWZ / (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→24.53 Å / Num. obs: 19371 / % possible obs: 99.9 % / Redundancy: 10.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.091 / Rrim(I) all: 0.199 / Net I/σ(I): 8.2
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 1398 / CC1/2: 0.889

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E2E

5e2e


Resolution: 2→24.53 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.886 / SU B: 5.27 / SU ML: 0.148 / Cross valid method: FREE R-VALUE / ESU R: 0.201 / ESU R Free: 0.19
RfactorNum. reflection% reflection
Rfree0.2706 940 4.853 %
Rwork0.2067 18430 -
all0.21 --
obs-19370 99.871 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.059 Å2
Baniso -1Baniso -2Baniso -3
1-2.467 Å20 Å20.961 Å2
2---1.27 Å2-0 Å2
3----1.344 Å2
Refinement stepCycle: LAST / Resolution: 2→24.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 31 176 2199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122059
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.8162799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6425259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.929519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69410342
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.0131088
X-RAY DIFFRACTIONr_chiral_restr0.1390.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021547
X-RAY DIFFRACTIONr_nbd_refined0.230.21004
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21424
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2140
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1680.2104
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2420.237
X-RAY DIFFRACTIONr_mcbond_it1.651.9411042
X-RAY DIFFRACTIONr_mcangle_it2.5113.4721299
X-RAY DIFFRACTIONr_scbond_it2.532.2431017
X-RAY DIFFRACTIONr_scangle_it3.8714.0061500
X-RAY DIFFRACTIONr_lrange_it7.29427.3743260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.372730.24513170.25113900.9060.9551000.232
2.052-2.1070.258720.23313220.23513940.9540.9581000.221
2.107-2.1680.3650.22613050.22913700.9450.9631000.212
2.168-2.2340.269760.22712230.22912990.9580.9631000.213
2.234-2.3070.33590.2211980.22612570.9330.9651000.208
2.307-2.3870.284690.22111350.22512040.9440.9641000.208
2.387-2.4760.285520.20711380.2111900.9470.971000.197
2.476-2.5760.337510.19611150.20211660.9430.9731000.185
2.576-2.690.265440.20310530.20610970.9550.9721000.193
2.69-2.8190.237530.2059890.20710420.9610.971000.197
2.819-2.9690.267510.2119430.2139950.9480.96999.89950.203
2.969-3.1470.322450.2139040.2189490.9310.9681000.209
3.147-3.360.235340.2098650.218990.9610.9691000.208
3.36-3.6240.252400.1947860.1978260.9470.9751000.196
3.624-3.9610.291260.1967360.1997660.9430.97499.47780.202
3.961-4.4140.204340.1936690.1937040.9710.97499.8580.196
4.414-5.0690.255410.1745720.1796130.9640.9791000.183
5.069-6.1430.273370.2124970.2165360.9540.97299.62690.219
6.143-8.4280.25150.2094060.2114220.9790.9799.7630.22
8.428-24.530.0830.1822570.1812650.9990.97798.11320.189

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